Variant report

Variant	rs10064744
Chromosome Location	chr5:58447190-58447191
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10070295	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10073292	0.96[ASN][1000 genomes]
rs1077978	0.91[CEU][hapmap]
rs12516263	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16889248	0.95[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16889254	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16889258	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17778950	0.90[CHB][hapmap]
rs1961	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs62356728	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6450505	0.83[CEU][hapmap]
rs6868963	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6869149	1.00[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6874089	0.95[CEU][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap]
rs6881137	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892369	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6896497	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7714707	1.00[CEU][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7716261	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7728221	0.95[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap]
rs7735375	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8180396	0.91[CEU][hapmap]
rs9292191	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv881702	chr5:58432413-58474854	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10064744	RAB3C	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58427200-58454000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr5:58429800-58447200	Weak transcription	Left Ventricle	heart
3	chr5:58433000-58451600	Weak transcription	Fetal Muscle Leg	muscle
4	chr5:58437400-58454000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:58439000-58484000	Weak transcription	Fetal Kidney	kidney
6	chr5:58440200-58448600	Weak transcription	Brain Anterior Caudate	brain
7	chr5:58442400-58448600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr5:58443000-58447400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr5:58443000-58447600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr5:58444000-58449800	Genic enhancers	A549	lung
11	chr5:58444800-58448000	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr5:58444800-58448400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr5:58445400-58447200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:58445800-58447400	Strong transcription	Hela-S3	cervix
15	chr5:58445800-58448000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr5:58446000-58447200	Weak transcription	Psoas Muscle	Psoas
17	chr5:58446000-58447400	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:58446000-58448000	Enhancers	Fetal Intestine Small	intestine
19	chr5:58446000-58448600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:58446200-58447400	Weak transcription	Small Intestine	intestine
21	chr5:58446200-58448400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr5:58446200-58449000	Enhancers	Fetal Intestine Large	intestine
23	chr5:58446600-58447600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr5:58446600-58447800	Enhancers	Fetal Heart	heart
25	chr5:58446800-58449200	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr5:58447000-58447200	Enhancers	Stomach Mucosa	stomach
27	chr5:58447000-58447600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr5:58447000-58447600	Enhancers	Right Ventricle	heart
29	chr5:58447000-58447600	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr5:58447000-58447600	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr5:58447000-58447800	Enhancers	HepG2	liver
32	chr5:58447000-58449400	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr5:58447000-58450000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:58447000-58453400	Enhancers	Primary T cells from cord blood	blood

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